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STACKS_trabalhando.sh
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STACKS_trabalhando.sh
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/share/programs/stacks/bin/cstacks -b 1 -o /PATH/TO/Stacks/RESULTS_new3/ -p 15 -n 2 \
-s /PATH/TO/Stacks/RESULTS_new3/A_RS7 \
-s /PATH/TO/Stacks/RESULTS_new3/A_RS8 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_1 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_2 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_3 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_4 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_5 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_6 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_7 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_8 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_9 \
-s /PATH/TO/Stacks/RESULTS_new3/GO30_1 \
-s /PATH/TO/Stacks/RESULTS_new3/GO30_2 \
-s /PATH/TO/Stacks/RESULTS_new3/GO30_3 \
-s /PATH/TO/Stacks/RESULTS_new3/GO30_4 \
-s /PATH/TO/Stacks/RESULTS_new3/GO30_5 \
-s /PATH/TO/Stacks/RESULTS_new3/GO30_6 \
-s /PATH/TO/Stacks/RESULTS_new3/GO30_7 \
-s /PATH/TO/Stacks/RESULTS_new3/GO30_8 \
-s /PATH/TO/Stacks/RESULTS_new3/GO30_9 \
-s /PATH/TO/Stacks/RESULTS_new3/GO31_1 \
-s /PATH/TO/Stacks/RESULTS_new3/GO31_2 \
-s /PATH/TO/Stacks/RESULTS_new3/GO31_3 \
-s /PATH/TO/Stacks/RESULTS_new3/GO31_4 \
-s /PATH/TO/Stacks/RESULTS_new3/GO31_5 \
-s /PATH/TO/Stacks/RESULTS_new3/GO31_6 \
-s /PATH/TO/Stacks/RESULTS_new3/GO31_7 \
-s /PATH/TO/Stacks/RESULTS_new3/GO31_8 \
-s /PATH/TO/Stacks/RESULTS_new3/GO31_9 \
-s /PATH/TO/Stacks/RESULTS_new3/MG20_1 \
-s /PATH/TO/Stacks/RESULTS_new3/MG20_2 \
-s /PATH/TO/Stacks/RESULTS_new3/MG20_3 \
-s /PATH/TO/Stacks/RESULTS_new3/MG20_4 \
-s /PATH/TO/Stacks/RESULTS_new3/MG20_5 \
-s /PATH/TO/Stacks/RESULTS_new3/MG20_6 \
-s /PATH/TO/Stacks/RESULTS_new3/MG20_7 \
-s /PATH/TO/Stacks/RESULTS_new3/MG20_8 \
-s /PATH/TO/Stacks/RESULTS_new3/MG20_9 \
-s /PATH/TO/Stacks/RESULTS_new3/PR51_1 \
-s /PATH/TO/Stacks/RESULTS_new3/PR51_2 \
-s /PATH/TO/Stacks/RESULTS_new3/PR51_3 \
-s /PATH/TO/Stacks/RESULTS_new3/PR51_4 \
-s /PATH/TO/Stacks/RESULTS_new3/PR51_5 \
-s /PATH/TO/Stacks/RESULTS_new3/PR51_6 \
-s /PATH/TO/Stacks/RESULTS_new3/PR51_7 \
-s /PATH/TO/Stacks/RESULTS_new3/PR51_8 \
-s /PATH/TO/Stacks/RESULTS_new3/PR52_1 \
-s /PATH/TO/Stacks/RESULTS_new3/PR52_2 \
-s /PATH/TO/Stacks/RESULTS_new3/PR52_3 \
-s /PATH/TO/Stacks/RESULTS_new3/PR52_4 \
-s /PATH/TO/Stacks/RESULTS_new3/PR52_5 \
-s /PATH/TO/Stacks/RESULTS_new3/PR52_6 \
-s /PATH/TO/Stacks/RESULTS_new3/PR52_7 \
-s /PATH/TO/Stacks/RESULTS_new3/PR52_8 \
-s /PATH/TO/Stacks/RESULTS_new3/PR52_9 \
-s /PATH/TO/Stacks/RESULTS_new3/RS16_1 \
-s /PATH/TO/Stacks/RESULTS_new3/RS16_2 \
-s /PATH/TO/Stacks/RESULTS_new3/RS16_3 \
-s /PATH/TO/Stacks/RESULTS_new3/RS16_4 \
-s /PATH/TO/Stacks/RESULTS_new3/RS16_5 2>&1
/share/programs/stacks/bin/cstacks -b 1 -o /PATH/TO/Stacks/RESULTS_new3/ -p 15 -n 2 \
-s /PATH/TO/Stacks/RESULTS_new3/A_RS7 \
-s /PATH/TO/Stacks/RESULTS_new3/A_RS8 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_1 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_2 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_3 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_4 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_5 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_6 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_7 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_8 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_9 2>&1
/share/programs/stacks/bin/sstacks -b 1 -c /PATH/TO/Stacks/RESULTS_new3/batch_1 -o /PATH/TO/Stacks/RESULTS_new3/ \
-s /PATH/TO/Stacks/RESULTS_new3/A_RS7 \
-s /PATH/TO/Stacks/RESULTS_new3/A_RS8 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_1 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_2 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_3 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_4 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_5 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_6 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_7 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_8 \
-s /PATH/TO/Stacks/RESULTS_new3/BA34_9 2>&1
/share/programs/stacks/bin/populations -b 1 -P /PATH/TO/Stacks/RESULTS_new3 -s -t 15 -M /PATH/TO/Stacks/Barcodes_files/popmap3col.txt -t 15 -r 0.75 --fasta --fasta_strict --vcf --genepop --structure --plink --phylip --phylip_var --phylip_var_all 2>&1
ls -1 *.fastq.gz |
while read line;
do
echo -n "$line ";
zcat $line | sed -n '2~4p' |
awk '{print length}' | sort -n | uniq -c;
done